Julia 1.8 update

[fonsp]

Hello! 👋

This binder currently fails to build, I think this is happening because it is using Julia 1.8 during the build, but this environment was generated using Julia 1.6, and one of the pinned dependencies (RDatasets.jl) used internal Julia API (ccall) in a way that was not future-proof.

What I did to generate the files in this PR:

• Run julia --project inside the repo with Julia 1.8
• import Pkg
• Pkg.upgrade_manifest() (not strictly necessary, but Julia 1.7 started using a new format for Manifest.toml. You see a warning otherwise.)
• Pkg.update() (update all packages to latest and update Manifest.toml

You can test my branch with:

https://mybinder.org/v2/gh/fonsp/demo-julia/julia-18-update it works!

Logs from failing binder build on current `main`

Waiting for build to start...
[91m   Installed VersionParsing ── v1.3.0
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[0m[91m   Installed IJulia ────────── v1.24.0
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[0m[91m   Installed SnoopPrecompile ─ v1.0.3
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   Installed SoftGlobalScope ─ v1.1.0
[0m[91m    Updating `/srv/julia/pkg/environments/v1.8/Project.toml`
  [7073ff75] + IJulia v1.24.0
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   Installed DocStringExtensions ───────── v0.8.5
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[0m[91m┌ Warning: The active manifest file at `/home/jovyan/Manifest.toml` has an old format that is being maintained.
│ To update to the new format, which is supported by Julia versions ≥ 1.6.2, run `Pkg.upgrade_manifest()` which will upgrade the format without re-resolving.
│ To then record the julia version re-resolve with `Pkg.resolve()` and if there are resolve conflicts consider `Pkg.update()`.
â”” @ Pkg.Types /cache/build/default-amdci4-2/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/manifest.jl:287
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  [c8ffd9c3] ~ MbedTLS_jll ⇒ v2.28.0+0
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  [8e850ede] ~ nghttp2_jll ⇒ v1.48.0+0
  [3f19e933] ~ p7zip_jll ⇒ v17.4.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
[0m[91m┌ Warning: The Pkg REPL mode is intended for interactive use only, and should not be used from scripts. It is recommended to use the functional API instead.
â”” @ Pkg.REPLMode /cache/build/default-amdci4-2/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/REPLMode/REPLMode.jl:379
[0m[91mPrecompiling[0m[91m [0m[91mproject...[0m[91m
[0m[91m[32m  ✓ [39m[90mOpenBLAS_jll[39m[0m[91m
[0m[91m[32m  ✓ [39m[90mMKL_jll[39m[0m[91m
[0m[91m[32m  ✓ [39m[90mlibblastrampoline_jll[39m
[0m[91m[91m  ✗ [39m[90mSentinelArrays[39m
[0m[91m[91m  ✗ [39m[90mCSV[39m
[0m[91m[32m  ✓ [39m[90mFFTW[39m
[0m[91m[32m  ✓ [39m[90mKernelDensity[39m
[0m[91m[91m  ✗ [39mRDatasets
[0m[91m[32m  ✓ [39mGadfly
[0m[91m  6 dependencies successfully precompiled in 44 seconds. 78 already precompiled.
[0m[91m
[0m[91mERROR: [0m[91mThe following 1 direct dependency failed to precompile:

RDatasets [ce6b1742-4840-55fa-b093-852dadbb1d8b]

Failed to precompile RDatasets [ce6b1742-4840-55fa-b093-852dadbb1d8b] to /srv/julia/pkg/compiled/v1.8/RDatasets/jl_2O94e1.
ERROR: LoadError: ccall method definition: argument 1 type doesn't correspond to a C type
Stacktrace:
 [1] top-level scope
   @ /srv/julia/pkg/packages/SentinelArrays/VbnBp/src/SentinelArrays.jl:209
 [2] include
   @ ./Base.jl:419 [inlined]
 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
   @ Base ./loading.jl:1554
 [4] top-level scope
   @ stdin:1
in expression starting at /srv/julia/pkg/packages/SentinelArrays/VbnBp/src/SentinelArrays.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile SentinelArrays [91c51154-3ec4-41a3-a24f-3f23e20d615c] to /srv/julia/pkg/compiled/v1.8/SentinelArrays/jl_5HnZZo.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /srv/julia/pkg/packages/CSV/Zl2ww/src/CSV.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /srv/julia/pkg/compiled/v1.8/CSV/jl_htt4Dv.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /srv/julia/pkg/packages/RDatasets/eRbZP/src/RDatasets.jl:1
in expression starting at stdin:1[0m[91m
Stacktrace:[0m[91m
[0m[91m [1] pkgerror(msg::[0m[91mString)
   @ Pkg.Types [0m[91m/srv/julia/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67[0m[91m
[0m[91m [2] [0m[91mprecompile(ctx::[0m[91mPkg.Types.Context, pkgs[0m[91m::[0m[91mVector{String}; internal_call::[0m[91mBool, strict[0m[91m::Bool, warn_loaded::[0m[91mBool, already_instantiated::[0m[91mBool, kwargs::[0m[91mBase.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1435
 [3] precompile
   @ /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1072 [inlined]
 [4] #precompile#225
   @ /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1071 [inlined]
 [5] precompile (repeats 2 times)
   @ /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1071 [inlined]
 [6] do_cmd!(command::Pkg.REPLMode.Command, repl::Pkg.REPLMode.MiniREPL)
   @ Pkg.REPLMode [0m[91m/srv/julia/share/julia/stdlib/v1.8/Pkg/src/REPLMode/REPLMode.jl:406
 [7] do_cmd(repl::Pkg.REPLMode.MiniREPL, input::String; do_rethrow::Bool)
   @ Pkg.REPLMode /srv/julia/share/julia/stdlib/v1.8/Pkg/src/REPLMode/REPLMode.jl:387
 [8] top-level scope
   @ none:1
[0mRemoving intermediate container 2fac049b0a26
The command '/bin/sh -c JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); Pkg.resolve(); pkg"precompile"'' returned a non-zero code: 1